Neurite degeneration is a cellular dysfunction commonly associated with neurodegenerative pathologies such as Alzheimer’s disease and Parkinson’s disease (PD). One common method of scoring neurite degeneration in micrographs involves calculation of a degeneration index (DI) using neurite fragment measurements obtained via the particle analyzer plugin of FIJI software. However, this method can be time consuming and subject to inaccuracies related to inadequate contrast. Here we describe a modified method for performing DI measurements with enhanced efficiency, accessibility, and accuracy compared to existing techniques. We developed a macro to automate the analysis process, enabling rapid and objective measurements of multiple images. We have also increased the accuracy of measurements by modifying selection criteria for neurite fragments, as well as by determining optimal procedures for contrast enhancement and removal of non-neurite materials from images. Moreover, we demonstrate how this method may be applied to measure neurite degeneration in an in vitro model of PD. To model neurite degeneration associated with PD, we treated Lund Human Mesencephalic (LUHMES) cells with 4-hydroxynonenal or 6-hydroxydopamine, compounds that induce oxidative stress. We describe culture methods, cell densities, and drug concentrations that yield consistent and accurate measurements of neurite degeneration, and we demonstrate use of our optimized method in an experiment assessing the effects of c-Jun N-terminal Kinase (JNK) on neurite degeneration. Since neurite degeneration is a key, early-stage event associated with PD, this optimized and automated method may be used to gain novel insights into molecular interactions underlying PD progression.

Semester/Year of Award

Fall 2020


Bradley Kraemer

Mentor Department Affiliation

Biological Sciences

Access Options

Open Access Thesis

Document Type

Bachelor Thesis

Degree Name

Honors Scholars

Degree Level



Biological Sciences